Mercurial > repos > iuc > mothur_rename_seqs

annotate rename.seqs.xml @ 5:0a213cb7cb27 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author iuc
date Thu, 05 Nov 2020 22:19:27 +0000
parents 1ac1d3e02088
children 02a42e3fa758
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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1 <tool profile="16.07" id="mothur_rename_seqs" name="Rename.seqs" version="@WRAPPER_VERSION@.0">
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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2 <description>Rename sequences by concatenating the group name</description>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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3 <macros>
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4 <import>macros.xml</import>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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5 </macros>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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6 <expand macro="requirements"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$group' group.dat &&
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$name' name.dat &&
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$qfile' qfile.dat &&
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 ln -s '$contigsreport' contigsreport.dat &&
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 echo 'rename.seqs(
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 fasta=fasta.dat,
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 group=group.dat,
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #if $name:
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23 name=name.dat,
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #end if
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25 #if $qfile:
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26 qfile=qfile.dat,
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 #end if
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #if $contigsreport:
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 contigsreport=contigsreport.dat,
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #end if
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 placement=$placement
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 )'
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 | sed 's/ //g' ## mothur trips over whitespace
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 | mothur
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35 | tee mothur.out.log
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 ]]></command>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 <inputs>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 <param argument="fasta" type="data" format="fasta,mothur.align" label="Fasta file"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 <param argument="group" type="data" format="mothur.groups" label="Group file"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 <param argument="name" type="data" format="mothur.names" optional="true" label="Names file"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 <param argument="qfile" type="data" format="qual454" optional="true" label="quality file"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 <param argument="contigsreport" type="data" format="tabular" optional="true" label="Contigsreport file"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 <param argument="placement" type="select" label="Placement of group name">
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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44 <option value="back" selected="true">back</option>
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45 <option value="front">front</option>
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46 </param>
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47 <expand macro="param-savelog"/>
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48 </inputs>
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49 <outputs>
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50 <expand macro="logfile-output"/>
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51 <data name="group_renamed" format="mothur.groups" from_work_dir="group.renamed.dat" label="${tool.name} on ${on_string}: group_renamed"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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52 <data name="fasta_renamed" format_source="fasta" from_work_dir="fasta.renamed.dat" label="${tool.name} on ${on_string}: fasta_renamed"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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53 <data name="map" format="tabular" from_work_dir="fasta.renamed_map" label="${tool.name} on ${on_string}: renaming map"/>
1ac1d3e02088 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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54 <data name="name_renamed" format="mothur.names" from_work_dir="name.renamed.dat" label="${tool.name} on ${on_string}: name_renamed">
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55 <filter>name</filter>
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56 </data>
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57 <data name="qfile_renamed" format="qual454" from_work_dir="qfile.renamed.dat" label="${tool.name} on ${on_string}: qfile_renamed">
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58 <filter>qfile</filter>
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59 </data>
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60 <data name="contigsreport_renamed" format="tabular" from_work_dir="contigsreport.renamed.dat" label="${tool.name} on ${on_string}: contigsreport_renamed">
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61 <filter>contigsreport</filter>
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62 </data>
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63 </outputs>
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64 <tests>
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65 <test><!-- test with required params -->
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66 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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67 <param name="group" value="amazon.groups"/>
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68 <param name="name" value="amazon1.names"/>
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69 <output name="fasta_renamed" ftype="fasta">
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70 <assert_contents>
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71 <expand macro="test-fasta-format"/>
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72 <has_text text="42_forest"/>
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73 <has_text text="42_pasture"/>
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74 </assert_contents>
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75 </output>
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76 <output name="map" ftype="tabular">
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77 <assert_contents>
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78 <has_n_columns n="2"/>
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79 <has_line_matching expression="^42_forest\tU68631$"/>
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80 </assert_contents>
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81 </output>
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82 <output name="group_renamed" ftype="mothur.groups">
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83 <assert_contents>
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84 <has_n_columns n="2"/>
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85 <has_line_matching expression="^42_forest\tforest$"/>
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86 </assert_contents>
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87 </output>
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88 <output name="name_renamed" ftype="mothur.names">
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89 <assert_contents>
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90 <has_n_columns n="2"/>
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91 <has_line_matching expression="^42_forest\t42_forest$"/>
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92 </assert_contents>
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93 </output>
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94 <param name="savelog" value="true"/>
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95 <expand macro="logfile-test"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 @MOTHUR_OVERVIEW@
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101
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102 **Command Documentation**
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103
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104 The rename.seqs_ command takes fasta-formatted sequence file and group file, and renames
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105 the sequences by appending the group name to the sequence number.
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106
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107 .. _rename.seqs: https://www.mothur.org/wiki/Rename.seqs
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108
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109 ]]></help>
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110 <expand macro="citations"/>
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111 </tool>